Contacts of the strand formed by residues 50 - 57 (chain B) in PDB entry 5AYR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A LYS* 4.3 17.5 - - - +
29B GLU* 3.6 43.1 - - + +
30B GLU 3.6 9.0 - - - +
31B ILE* 4.1 20.2 - - + +
48B ASN 4.1 1.7 + - - +
49B LYS* 1.3 71.0 - - - +
51B LEU* 1.3 62.7 - - - +
52B GLN 4.2 0.5 + - - -
72B TYR 4.4 0.3 - - - +
73B TYR* 3.4 25.9 - - + -
74B GLN* 4.9 1.9 + - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE 3.6 1.2 - - - +
29B GLU* 3.3 7.7 - - - -
30B GLU 2.7 35.3 + - - +
32B ALA* 3.6 31.9 - - + -
35B ILE* 4.8 6.1 - - + -
36B LEU* 4.2 16.2 - - + -
46B LEU* 4.2 16.4 - - + -
49B LYS* 4.5 3.8 - - + +
50B ILE* 1.3 85.2 - - - +
52B GLN* 1.3 61.0 + - - +
53B THR* 4.0 12.0 - - + +
71B LEU* 4.5 16.2 - - + -
72B TYR 3.3 17.3 - - - +
73B TYR* 4.0 16.8 - - + -
78B ILE* 4.5 6.3 - - + -
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Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ASN* 2.9 42.4 + - - +
218A LYS* 5.3 2.6 - - - +
900A MG 4.2 0.6 - - - -
27B SER* 3.2 14.5 + - - +
28B ILE 3.5 27.3 + - - +
29B GLU* 3.2 25.6 - - - +
50B ILE 4.2 0.4 + - - -
51B LEU* 1.3 71.8 - - - +
53B THR* 1.3 61.1 + - - +
54B TYR* 3.9 18.2 - - + +
70B ILE 3.9 0.9 - - - +
71B LEU* 3.6 3.1 - - - -
72B TYR* 2.8 51.5 + - + +
74B GLN 4.9 6.8 - - - +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A SER* 5.1 0.9 + - - -
272A LEU* 3.5 21.2 - - + +
26B GLU 3.2 0.9 + - - +
27B SER* 3.0 26.9 + - - -
28B ILE* 2.9 37.6 + - - +
30B GLU 4.9 0.4 - - - +
35B ILE* 3.8 28.0 - - + +
51B LEU* 4.0 12.1 - - + +
52B GLN* 1.3 78.9 - - - +
54B TYR* 1.3 64.6 + - - +
55B THR* 4.7 2.1 + - - -
70B ILE 3.8 2.2 - - - -
71B LEU* 3.6 15.7 - - + -
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A HIS* 5.2 1.3 - + - -
214A ALA* 3.5 32.2 + - + +
215A ASN* 4.1 2.4 + - - -
25B CYS* 3.5 25.4 - - - -
26B GLU 3.3 4.0 - - - -
27B SER* 3.6 12.1 - - - -
52B GLN* 3.9 25.4 - - + +
53B THR* 1.3 73.5 - - - +
55B THR* 1.3 62.7 + - - +
56B TYR* 4.0 17.6 - - + +
69B PHE* 2.9 9.6 - - - +
70B ILE* 2.8 49.4 + - + +
72B TYR* 3.5 32.8 - + - -
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PRO* 4.0 21.1 - - + -
270A SER* 4.6 4.0 + - - -
271A PRO* 4.1 10.8 - - + -
272A LEU* 3.6 27.1 - - + +
25B CYS* 3.5 1.3 - - - -
26B GLU* 2.7 48.2 + - - +
53B THR* 4.7 1.2 + - - -
54B TYR* 1.3 74.4 + - - +
56B TYR* 1.3 66.5 + - - +
57B TYR* 3.8 2.9 - - - -
67B TYR* 3.9 22.9 - - + +
68B PRO 3.4 8.7 - - - +
69B PHE* 4.1 2.4 - - + +
83B ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU* 3.1 45.4 + - + +
7B LEU* 4.6 6.3 - - + -
23B TRP* 3.7 37.5 - + + -
24B GLU 3.3 15.5 - - - +
25B CYS* 3.9 22.3 - - + -
54B TYR* 4.0 25.8 - - + +
55B THR* 1.3 73.4 - - - +
57B TYR* 1.3 63.1 + - - +
61B LEU* 4.1 2.6 - - - +
67B TYR* 3.6 18.0 - - - -
68B PRO* 2.8 41.5 + - + +
69B PHE* 4.4 0.2 - - - -
70B ILE* 3.8 28.6 - - + +
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 4.6 2.1 - + - -
152A GLN* 2.9 25.8 + - - -
160A VAL* 4.8 0.3 - - - +
165A PRO* 3.8 14.8 + - + -
166A PRO 3.7 14.4 - - - -
167A PRO* 3.6 21.1 - - + +
168A PRO* 3.3 26.7 - - + -
23B TRP* 3.6 1.7 - - - -
24B GLU* 2.9 59.3 + - + +
25B CYS 3.7 17.9 - - - -
26B GLU* 3.9 2.5 - - + -
55B THR 3.8 7.9 - - - -
56B TYR* 1.3 76.2 - - - +
58B SER* 1.3 65.7 + - - +
61B LEU* 3.8 11.6 - - - +
62B HIS* 3.7 32.3 - + + -
67B TYR* 4.2 4.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il